SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations,Journal of Chemical Theory and Computation

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SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2021-10-18 , DOI: 10.1021/acs.jctc.1c00431
Sun-Ting Tsai ₁ , Zachary Smith ₂ , Pratyush Tiwary ₃

Affiliation

Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems, especially in situations with multiple competing pathways. When these high-dimensional systems are projected on low-dimensional coordinates, which are often needed for enhanced sampling or for interpretation of simulations and experiments, one can end up losing the kinetic connectivity of the underlying high-dimensional landscape. Thus, in the low-dimensional projection, metastable states might appear closer or further than they actually are. To deal with this issue, in this work, we develop a formalism that learns a multidimensional yet minimally complex reaction coordinate (RC) for generic high-dimensional systems. When projected along this RC, all possible kinetically relevant pathways can be demarcated and the true high-dimensional connectivity is maintained. One of the defining attributes of our method lies in that it can work on long unbiased simulations as well as biased simulations often needed for rare event systems. We demonstrate the utility of the method by studying a range of model systems including conformational transitions in a small peptide Ace-Ala₃-Nme, where we show how two-dimensional and three-dimensional RCs found by our previously published spectral gap optimization method “SGOOP” [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci.2016,113, 2839] can capture the kinetics for 23 and all 28 out of the 28 dominant state-to-state transitions, respectively.

中文翻译：

SGOOP-d：从有偏/无偏模拟估计稀有事件系统的动力学距离和反应坐标维数

了解包括反应途径和相关转变速率在内的动力学是众多化学和生物系统中的一个重要但困难的问题，尤其是在具有多个竞争途径的情况下。当这些高维系统被投影到低维坐标上时，通常需要增强采样或解释模拟和实验，最终可能会失去潜在高维景观的动力学连接。因此，在低维投影中，亚稳态可能看起来比实际更近或更远。为了解决这个问题，在这项工作中，我们开发了一种形式主义，可以学习通用高维系统的多维但最小复杂反应坐标（RC）。当沿着这个 RC 投影时，可以标定所有可能的动力学相关路径，并保持真正的高维连接。我们方法的定义属性之一在于它可以用于长时间的无偏模拟以及罕见事件系统通常需要的有偏模拟。我们通过研究一系列模型系统（包括小肽 Ace-Ala 中的构象转换）来证明该方法的实用性₃ -Nme，我们展示了如何通过我们之前发布的光谱间隙优化方法“SGOOP”[Tiwary, P. and Berne, BJ Proc. 纳特尔。阿卡德。科学。2016, 113 , 2839] 可以分别捕获 28 个主要状态到状态转换中的 23 个和所有 28 个的动力学。

更新日期：2021-11-09

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